Subject: PROSPECT 1.0 is available

From: Dong Xu <[email-masked]>
Date: Fri, 15 Dec 2000 18:34:07 -0500

Announcement: Version 1.0 of PROSPECT
=====================================

The Computational Protein Structure Group of Oak Ridge National
Laboratory would like to announce the release of PROSPECT Version
1.0.
PROSPECT (PROtein Structure Prediction and Evaluation Computer
Toolkit)
is a threading-based protein structure prediction system. PROSPECT
is
particularly designed to recognize structural folds whose sequence
have
no significant homology to the target sequence. For detailed
information
about PROSPECT, please check
             http://compbio.ornl.gov/structure/prospect/

PROSPECT has a number of unique features --

  * The system guarantees to find the globally optimal alignments
    for a given energy function with any combination of the
following
    terms: (1) mutation energy (including position-specific score
    matrix derived from multiple-sequence alignments), (2) singleton

    energy (including matching scores to the predicted secondary
    structures), (3) pairwise contact potential (distance dependent
or
    independent), and (4) alignment gap penalties.

  * The system allows users to easily incorporate biological
knowledge
    and constraints into the threading process to find optimal
    alignments under the specified constraints, which may include:
        - specified disulfide bonds
        - specified active sites
        - specified secondary structures
        - specified NOE restraints in NMR
        - specified gaps with no gap penalties

  * The system provides a prediction confidence assessment for each
    prediction  based on a neural-net method and an evaluation of
    compactness of the predicted structure.

  * A Web-based interface is available to browse the threading
    alignments and 3D structures.

PROSPECT is free of charge to academic users. Please contact the
authors
(Ying Xu at [email-masked] or Dong Xu at [email-masked]) about the
download
information. For commercial users, please contact the authors for
licensing information.

Reference:
Ying Xu and Dong Xu. Protein threading using PROSPECT:
Design and evaluation. Proteins: Structure, Function, and Genetics.
40:343-354. 2000.